[Taxacom] clique analysis in texbooks

Richard Jensen rjensen at saintmarys.edu
Fri Aug 12 09:48:22 CDT 2011

Sometimes we can "guess better".  Years ago, before the development of 
PAUP and other more sophisticated software, I used the then current 
version (mainframe) of Steve Farris' parsimony program to create a 
phylogeny for oaks.  I was able, by "intuitive" branch swapping, to 
create a more parsimonious tree than was generated by the software.  Of 
course, today's algorithms do this for us to generate (with small data 
sets) THE most parsimonious tree(s) for the data.

"Fiddling" is ok, as long as one provides a sound rationale for the 
fiddling.  I'm not sure what Nero's rationale was, although much was 
lost because he did fiddle around!

On 8/12/2011 9:59 AM, Richard Petit wrote:
>> IMO, morphological cladograms, if you fiddle with them enough, can make
>> a fine natural key. This would be good guidance to evolutionary
>> relationships, and one might expect such morphological relationships to
>> be different from the relationships in molecular trees for reasons I've
>> gone on and on about.
> This demonstrates the analogy I brought up a year or two ago about weighing pigs. "Fiddling" with a cladogram is exactly the same as "taking out rocks you might have guessed wrong and replacing them with rocks you think you can guess better."
> dick p.
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Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674

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